← Back to search
1qvp

C terminal SH3-like domain from Diphtheria toxin Repressor residues 144-226.

Method: SOLUTION NMR Dmax: 50.7 Å Quality: GOOD
▼

1. Protein Identity and Related Structures Protein Identity & Related Structures

Diphtheria toxin repressor

Corynebacterium diphtheriae

UniProt P33120

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 144–226 Fragment：Residues 144-226 No other associated polymer SOLUTION NMR NMR measurement conditions：pH 6.5；303 K；Pressure ambient NMR sample composition：1-2 mM DtxR144-226 U-15N; 10mM Potassium Phosphate buffer pH6.5 | 90% H2O/10% D2O NMR sample composition：1-2 mM DtxR144-226 U-15N and U-13C; 10mM Potassium Phosphate buffer pH6.5 | 90% H2O, 10% D2O; 100% D2O Resolution not provided

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 1QVP Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1BI0 STRUCTURE OF APO-AND HOLO-DIPHTHERIA TOXIN REPRESSOR Deposited 1998-06-21 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–226（226 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.5；pH 8.5
Resolution 2.30 Å R-free 0.296
1BI1 STRUCTURE OF APO-AND HOLO-DIPHTHERIA TOXIN REPRESSOR Deposited 1998-06-21 Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–226（226 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.5；pH 8.5
Resolution 2.20 Å R-free 0.311
1BI2 STRUCTURE OF APO-AND HOLO-DIPHTHERIA TOXIN REPRESSOR Deposited 1998-06-21 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–226（226 aa）
Chain B 1–226（226 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.5；pH 8.5
Resolution 2.30 Å R-free 0.352
1BI3 STRUCTURE OF APO-AND HOLO-DIPHTHERIA TOXIN REPRESSOR Deposited 1998-06-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–226（226 aa）
Chain B 1–226（226 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 2 SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.5；pH 8.5
Resolution 2.40 Å R-free 0.333
1BYM SOLUTION STRUCTURES OF THE C-TERMINAL DOMAIN OF DIPHTHERIA TOXIN REPRESSOR Deposited 1998-10-17 Different construct Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 130–226（97 aa） Fragment：RESIDUES 130-226
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；303 K
Resolution not provided
1C0W CRYSTAL STRUCTURE OF THE COBALT-ACTIVATED DIPHTHERIA TOXIN REPRESSOR-DNA COMPLEX REVEALS A METAL BINDING SH-LIKE DOMAIN Deposited 1999-07-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 4 PDB declaration: hexameric
Chain A 2–226（225 aa）
Chain B 2–226（225 aa）
Chain C 2–226（225 aa）
Chain D 2–226（225 aa）
Not recorded CO COBALT (II) ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 3.20 Å R-free 0.279
1DDN DIPHTHERIA TOX REPRESSOR (C102D MUTANT)/TOX DNA OPERATOR COMPLEX Deposited 1998-06-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 4 PDB declaration: hexameric
Chain A 1–226（226 aa）
Chain B 1–226（226 aa）
Chain C 1–226（226 aa）
Chain D 1–226（226 aa）
Mutation：C102D Mutation：C102D Mutation：C102D Mutation：C102D NI NICKEL (II) ION × 8 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 3.00 Å R-free 0.280
1DPR STRUCTURES OF THE APO-AND METAL ION ACTIVATED FORMS OF THE DIPHTHERIA TOX REPRESSOR FROM CORYNEBACTERIUM DIPHTHERIAE Deposited 1995-02-06 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–226（226 aa）
Chain B 1–226（226 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 3.00 Å R-free 0.417
1F5T DIPHTHERIA TOX REPRESSOR (C102D MUTANT) COMPLEXED WITH NICKEL AND DTXR CONSENSUS BINDING SEQUENCE Deposited 2000-06-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 4 PDB declaration: hexameric
Chain A 1–121（121 aa）
Chain B 1–121（121 aa）
Chain C 1–121（121 aa）
Chain D 1–121（121 aa）
Mutation：C102D Mutation：C102D Mutation：C102D Mutation：C102D NI NICKEL (II) ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；100 mM sodium cacodylate pH7.3, 10 mM MgCl2, 2 mM spermine, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 3.00 Å R-free 0.273
1FWZ GLU20ALA DTXR Deposited 2000-09-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–226（226 aa）
Mutation：E20A Non-standard monomer：Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 2 ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；1.6-2.0 ammonium sulfate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.30 Å R-free 0.285
1G3S CYS102SER DTXR Deposited 2000-10-25 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–226（226 aa）
Mutation：C102S No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；298 K；Ammonium sulfate, EDTA, glycerol, pH 8.5, VAPOR DIFFUSION, temperature 298K
Resolution 2.40 Å R-free 0.271
1G3T CYS102SER DTXR Deposited 2000-10-25 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–226（226 aa）
Chain B 1–226（226 aa）
Mutation：C102S Mutation：C102S No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；Ammonium sulfate, glycerol, EDTA, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.35 Å R-free 0.318
1G3W CD-CYS102SER DTXR Deposited 2000-10-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–226（226 aa）
Mutation：C102 CD CADMIUM ION × 2 SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；Ammonium sulfate, glycerol, CdCl2, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.40 Å R-free 0.259
1G3Y ARG80ALA DTXR Deposited 2000-10-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–226（226 aa）
Mutation：R80A ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；Ammonium sulfate, Zn2+, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.80 Å R-free 0.328
1P92 Crystal Structure of (H79A)DtxR Deposited 2003-05-08 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–226（226 aa）
Mutation：H79A BME BETA-MERCAPTOETHANOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；PEG 400, ammonium sulfate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.10 Å R-free 0.280
1P92 Crystal Structure of (H79A)DtxR Deposited 2003-05-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–226（226 aa）
Mutation：H79A BME BETA-MERCAPTOETHANOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；PEG 400, ammonium sulfate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.10 Å R-free 0.280
1QW1 Solution Structure of the C-Terminal Domain of DtxR residues 110-226 Deposited 2003-08-29 Different construct Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 110–226（117 aa） Fragment：RESIDUES 110-226
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；303 K；Pressure ambient
NMR sample composition 1-2 mM DtxR110-226 U-15N, 50 mM Potassium Phosphate, pH 6.5 | 90% H2O/10% D2O
NMR sample composition 1-2 mM DtxR110-226 U-15N U-13C, 50 mM Potassium Phosphate, pH 6.5 | 100% D2O
NMR sample composition 1-2 mM DtxR110-226 U-15N U-13C, 50 mM Potassium Phosphate, pH 6.5 | 90% H2O/10% D2O
Resolution not provided
1XCV Crystal Structure Of (H79AC102D)Dtxr complexed with Nickel(II) Deposited 2004-09-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–139（139 aa）
Mutation：H79A, C102D NI NICKEL (II) ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；ammonium sulfate, PEG 400, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.10 Å R-free 0.300
2DTR STRUCTURE OF DIPHTHERIA TOXIN REPRESSOR Deposited 1996-07-26 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–226（226 aa）
Not recorded SO4 SULFATE ION × 2 CO COBALT (II) ION × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.90 Å
2QQ9 Crystal Structure of DtxR(D6A C102D) Complexed with Nickel(II) Deposited 2007-07-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–226（226 aa）
Mutation：D6A, C102D NI NICKEL (II) ION × 4 PO4 PHOSPHATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；0.2 M Sodium Phosphate, 20% PEG 3350, 5 mM Nickel Chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.71 Å R-free 0.291
2QQA Crystal Structure of DtxR(E9A C102D) Complexed with Nickel(II) Deposited 2007-07-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–226（226 aa）
Mutation：E9A, C102D NI NICKEL (II) ION × 4 PO4 PHOSPHATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；0.2 M Sodium Phosphate, 20% PEG 3350, 5 mM Nickel Chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.10 Å R-free 0.256
2QQB Crystal Structure of DtxR(M10A C102D) Complexed with Nickel(II) Deposited 2007-07-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–226（226 aa）
Mutation：M10A, C102D NI NICKEL (II) ION × 4 PO4 PHOSPHATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；0.2 M Sodium Phosphate, 20% PEG 3350, 5 mM Nickel Chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.92 Å R-free 0.311
2TDX DIPHTHERIA TOX REPRESSOR (C102D MUTANT) COMPLEXED WITH NICKEL Deposited 1998-06-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–226（226 aa）
Mutation：C102D NI NICKEL (II) ION × 4 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.40 Å R-free 0.321
3GLX Crystal Structure Analysis of the DtxR(E175K) complexed with Ni(II) Deposited 2009-03-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–226（226 aa）
Mutation：E175K NI NICKEL (II) ION × 2 PO4 PHOSPHATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；0.95 M Sodium/Potasium Phosphate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.85 Å R-free 0.271

23 other PDB entries and 24 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name DTXR_CORDI
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 5–87； UniProt 144–226

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 1qvp

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1qvp
Download Download
▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id1qvp
Deposition date deposition_date2003-08-28
Structure title titleC terminal SH3-like domain from Diphtheria toxin Repressor residues 144-226.
Keywords keywords;REPRESSOR, DTXR, C-TERMINAL DOMAIN, PROKARYOTIC SH3 DOMAIN, TRANSCRIPTION REGULATION, PEPTIDE-BINDING, GENE REGULATION, DNA BINDING PROTEIN ;; DNA BINDING PROTEIN
Experimental Method methodSOLUTION NMR
▼

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier13.63 Å
Radius of gyration Rg (electron density) rg_electron13.06 Å
Forward intensity I(0) i0244533000.00
Molecular weight molecular_weight125300.0 kDa
Excluded volume excluded_volume154750 ų
Envelope volume envelope_volume28158 ų
Hydration-shell volume shell_volume15115 ų
Envelope diameter envelope_diameter53.8 Å
Shell Rg shell_rg21.89 Å
Envelope Rg envelope_rg16.11 Å
Shape Rg shape_rg13.03 Å
Total Rg total_rg13.48 Å
Total atoms total_atoms17563
Residues n_residues1131
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax50.7 Å
Rg (real space) rg_real13.60 Å
Rg uncertainty (real space) rg_real_error0.42 Å
I(0) (real space) i0_real2.4450e+08
I(0) uncertainty (real space) i0_real_error2.8230e+06
Rg (reciprocal space) rg_reciprocal13.60 Å
I(0) (reciprocal space) i0_reciprocal244500000.0000
Solution quality estimate total_estimate0.8167
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary16.7 Å
Skewness Skewness skewness0.332
Kurtosis Kurtosis kurtosis-0.044
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha461900.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.563; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.928; Smooth: 0.997
▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (1)

▼

7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd1qvpa1
Class classb — All beta proteins
Fold Fold foldb.34 — SH3-like barrel
Superfamily Superfamily superfamilyb.34.1 — C-terminal domain of transcriptional repressors
Family Family familyb.34.1.2 — FeoA-like
Domain ID domain_idd1qvpa2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (1 domains)

Domain ID domain_id1qvpA00
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology30 — SH3 type barrels.
Homologous superfamily homologous superfamily90 — Ferrous iron transport protein A (FeoA)
▶

8. Citations (1)

▶

9. Files and Curves (10)